After the movie, that's where Sunbow's take on the series ended. Another company picked it up, can't remember who, and made new episodes that came after the movie. The first 5 episodes was called the "The Firefly something or other." Can't remember the whole title. But in that story arc is where the Baroness and Dr. Mindbender I believe through some kind of magic or science were able to change Cobra Commander back. Once he was changed back, CC went with the hooded look that we see today. As for the comic series, I'm not sure how his look changed. I'm not even sure if the movie was incorporated into the comics or not.
I've read a lot of opinions about the episodes after the movie over the years, and most everyones opinion was that they weren't good once Sunbow's reign on G.I. Joe was over. They all seemed to lack something.
I've just recently acquired all the episodes on tape, but there all not in order and I haven't gotten to any of the post movie episodes yet. But that's pretty much the run down on Cobra Commander. I'm looking forward to hopefully seeing Serpentor return to the new G.I. Joe comics and hopefully the new toy line.
The Clown Prince
"All you have to decide is what to do with the time that is given to you." -Gandalf in 'The Fellowship of the Ring'